Man pages for USEPA/CompTox-ToxCast-tcpl
ToxCast Data Analysis Pipeline

assay_funcsFunctions for loading assay information
blineShiftShift the baseline to 0
chdatChemical library of tested chemicals in the example datasets...
config_funcsFunctions for configuring the tcpl package
dot-buildAssayQGenerate query for assay information
dot-convertNamesConvert assay names to their abbreviations
dot-load6DRLoad data for tcpl6
dot-plateHeatPlot plate heatmap
dot-prepFieldPaste appropriate table name to field name
flareFuncCalculate the weighted mean of a square to detect plate...
hill_utilsFunctions to solve the Hill model
interlaceFuncCalculate the weighted mean of a square to detect interlace...
is.oddCheck for odd numbers
luAbbreviation for 'length(unique(x))'
lwAbbreviation for 'length(which(x))'
mc1Perform level 1 multiple-concentration processing
mc2Perform level 2 multiple-concentration processing
MC2_MethodsList of level 2 multiple-concentration correction functions
mc3Perform level 3 multiple-concentration processing
MC3_MethodsList of level 3 multiple-concentration normalization methods
mc4Perform level 4 multiple-concentration processing
MC4_MethodsList of level 4 multiple-concentration methods for...
mc5Perform level 5 multiple-concentration processing
MC5_MethodsLoad list of level 5 multiple-concentration cutoff methods
mc6Perform level 6 multiple-concentration processing
MC6_MethodsLoad list of level 6 multiple-concentration flag methods
mcdatA subset of ToxCast data showing changes in the activity of...
ModelsModel objective functions
mthd_funcsFunctions for managing processing methods
query_funcsWrappers for sending queries and fetching results
registerMthdAdd a new analysis method
rgstr_funcsFunctions for registering & updating annotation information
sc1Perform level 1 single-concentration processing
SC1_MethodsList of level 1 single-concentration normalization functions
sc2Perform level 2 single-concentration processing
SC2_MethodsList of level 2 single-concentration hit-call functions
scdatA subset of ToxCast data showing changes in transcription...
sink.resetReset all sinks
tcplAddModelDraw a tcpl Model onto an existing plot
tcplAICProbCalculate the AIC probabilities
tcplAppendAppend rows to a table
tcplCascadeDo a cascading delete on tcpl screening data
tcplCode2CASNConvert chemical code to CAS Registry Number
tcplCytoPtCalculate the cytotoxicity point based on the "burst"...
tcpldbStatsGet summary statisitcs for the database
tcplDeleteDelete rows from tcpl databases
tcplFitFit the data with the constant, hill, and gain-loss models
tcplGetAeidget Aeid for endpoint name
tcplListFldsLoad the field names for a table
tcplLoadChemLoad sample/chemical information
tcplLoadClibLoad chemical library information
tcplLoadDataLoad tcpl data
tcplLoadUnitLoad response units for assay endpoints
tcplLvlCountLoad tcpl level counts
tcplMakeAeidMultiPltsCreate a .pdf with all dose-response plots for a given aeid,...
tcplMakeAeidPltsCreate a .pdf with dose-response plots
tcplMakeChidMultiPltsCreate a .pdf with all dose-response plots for a given chid,...
tcplMultiplotPlot summary fits based on fit and dose-response data
tcplPlotFitcPlot the fit category tree
tcplPlotFitsPlot summary fits based on fit and dose-response data
tcplPlotM4IDPlot fit summary plot by m4id
tcplPlotPlatePlot plate heatmap
tcplPrepOtptMap assay/chemical ID values to annotation information
tcplRunPerform data processing
tcplSubsetChidSubset level 5 data to a single sample per chemical
tcplVarMatCreate chemical by assay matrices
tcplWriteDataWrite screening data into the tcpl databases
tcplWriteLvl0Write level 0 screening data into the tcpl databases
USEPA/CompTox-ToxCast-tcpl documentation built on March 1, 2019, 9:20 p.m.